5 Methods for Association Studies
115
Chen GK, Witte JS (2007) Enriching the analysis of genomewide association studies with
hierarchical modeling. Am J Hum Genet 81:397–404
Chen H, Lumley T, Brody J et al (2014) Sequence kernel association test for survival traits. Genet
Epidemiol 38:191–197
Chen H, Huffman JE, Brody JA et al (2019) Efficient variant set mixed model association tests for
continuous and binary traits in large-scale whole-genome sequencing studies. Am J Hum Genet
104:260–274
Choi M, Scholl UI, Ji W et al (2009) Genetic diagnosis by whole exome capture and massively
parallel DNA sequencing. Proc Natl Acad Sci USA 106:19096–19101
Clarke GM, Anderson CA, Pettersson FH, Cardon LR, Morris AP, Zondervan KT (2011) Basic
statistical analysis in genetic case-control studies. Nat Protoc 6:121–133
Claussnitzer M, Cho JH, Collins R et al (2020) A brief history of human disease genetics. Nature
577:179–189
Clayton DG (2009) Sex chromosomes and genetic association studies. Genome Med 1:110
Cordell HJ, Clayton DG (2005) Genetic association studies. Lancet 366:1121–1131
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype
structure in the human genome. Nat Genet 29:229–232
Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004
Dick DM, Agrawal A, Keller MC et al (2015) Candidate gene-environment interaction research:
reflections and recommendations. Perspect Psychol Sci 10:37–59
Dinu I, Potter JD, Mueller T et al (2009) Gene-set analysis and reduction. Brief Bioinform 10:24–
34
Dutta D, Scott L, Boehnke M, Lee S (2019) Multi-SKAT: general framework to test for rare-variant
association with multiple phenotypes. Genet Epidemiol 43:4–23
Elbers CC, van der Schouw YT, Wijmenga C, Onland-Moret NC (2009a) Comment on: Perry et al.
(2009) interrogating type 2 diabetes genome-wide association data using a biological pathwaybased approach. Diabetes 58:1463–1467. e9; author reply e10
Elbers CC, van Eijk KR, Franke L et al (2009b) Using genome-wide pathway analysis to unravel
the etiology of complex diseases. Genet Epidemiol 33:419–431
Evangelou E, Ioannidis JPA (2013) Meta-analysis methods for genome-wide association studies
and beyond. Nat Rev Genet 14:379–389
Evangelou M, Dudbridge F, Wernisch L (2014) Two novel pathway analysis methods based on a
hierarchical model. Bioinformatics 30:690–697
Evangelou E, Warren HR, Mosen-Ansorena D et al (2018) Genetic analysis of over 1 million
people identifies 535 new loci associated with blood pressure traits. Nat Genet 50:1412–1425
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus
genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Fehringer G, Kraft P, Pharoah PD et al (2016) Cross-cancer genome-wide analysis of lung,
ovary, breast, prostate, and colorectal cancer reveals novel pleiotropic associations. Cancer Res
76:5103–5114
Frazer KA, Ballinger DG, Cox DR et al (2007) A second generation human haplotype map of over
3.1 million SNPs. Nature 449:851–861
Frazer KA, Murray SS, Schork NJ, Topol EJ (2009) Human genetic variation and its contribution
to complex traits. Nat Rev Genet 10:241–251
Gabriel SB, Schaffner SF, Nguyen H et al (2002) The structure of haplotype blocks in the human
genome. Science 296:2225–2229
Gamazon ER, Wheeler HE, Shah KP et al (2015) A gene-based association method for mapping
traits using reference transcriptome data. Nat Genet 47:1091–1098
Genovese CR, Roeder K, Wasserman L (2006) False discovery control with p-value weighting.
Biometrika 93:509–524
Gilbert W, Maxam A (1973) The nucleotide sequence of the lac operator. Proc Natl Acad Sci USA
70:3581–3584
Gnirke A, Melnikov A, Maguire J et al (2009) Solution hybrid selection with ultra-long
oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189
115
Chen GK, Witte JS (2007) Enriching the analysis of genomewide association studies with
hierarchical modeling. Am J Hum Genet 81:397–404
Chen H, Lumley T, Brody J et al (2014) Sequence kernel association test for survival traits. Genet
Epidemiol 38:191–197
Chen H, Huffman JE, Brody JA et al (2019) Efficient variant set mixed model association tests for
continuous and binary traits in large-scale whole-genome sequencing studies. Am J Hum Genet
104:260–274
Choi M, Scholl UI, Ji W et al (2009) Genetic diagnosis by whole exome capture and massively
parallel DNA sequencing. Proc Natl Acad Sci USA 106:19096–19101
Clarke GM, Anderson CA, Pettersson FH, Cardon LR, Morris AP, Zondervan KT (2011) Basic
statistical analysis in genetic case-control studies. Nat Protoc 6:121–133
Claussnitzer M, Cho JH, Collins R et al (2020) A brief history of human disease genetics. Nature
577:179–189
Clayton DG (2009) Sex chromosomes and genetic association studies. Genome Med 1:110
Cordell HJ, Clayton DG (2005) Genetic association studies. Lancet 366:1121–1131
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype
structure in the human genome. Nat Genet 29:229–232
Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004
Dick DM, Agrawal A, Keller MC et al (2015) Candidate gene-environment interaction research:
reflections and recommendations. Perspect Psychol Sci 10:37–59
Dinu I, Potter JD, Mueller T et al (2009) Gene-set analysis and reduction. Brief Bioinform 10:24–
34
Dutta D, Scott L, Boehnke M, Lee S (2019) Multi-SKAT: general framework to test for rare-variant
association with multiple phenotypes. Genet Epidemiol 43:4–23
Elbers CC, van der Schouw YT, Wijmenga C, Onland-Moret NC (2009a) Comment on: Perry et al.
(2009) interrogating type 2 diabetes genome-wide association data using a biological pathwaybased approach. Diabetes 58:1463–1467. e9; author reply e10
Elbers CC, van Eijk KR, Franke L et al (2009b) Using genome-wide pathway analysis to unravel
the etiology of complex diseases. Genet Epidemiol 33:419–431
Evangelou E, Ioannidis JPA (2013) Meta-analysis methods for genome-wide association studies
and beyond. Nat Rev Genet 14:379–389
Evangelou M, Dudbridge F, Wernisch L (2014) Two novel pathway analysis methods based on a
hierarchical model. Bioinformatics 30:690–697
Evangelou E, Warren HR, Mosen-Ansorena D et al (2018) Genetic analysis of over 1 million
people identifies 535 new loci associated with blood pressure traits. Nat Genet 50:1412–1425
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus
genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Fehringer G, Kraft P, Pharoah PD et al (2016) Cross-cancer genome-wide analysis of lung,
ovary, breast, prostate, and colorectal cancer reveals novel pleiotropic associations. Cancer Res
76:5103–5114
Frazer KA, Ballinger DG, Cox DR et al (2007) A second generation human haplotype map of over
3.1 million SNPs. Nature 449:851–861
Frazer KA, Murray SS, Schork NJ, Topol EJ (2009) Human genetic variation and its contribution
to complex traits. Nat Rev Genet 10:241–251
Gabriel SB, Schaffner SF, Nguyen H et al (2002) The structure of haplotype blocks in the human
genome. Science 296:2225–2229
Gamazon ER, Wheeler HE, Shah KP et al (2015) A gene-based association method for mapping
traits using reference transcriptome data. Nat Genet 47:1091–1098
Genovese CR, Roeder K, Wasserman L (2006) False discovery control with p-value weighting.
Biometrika 93:509–524
Gilbert W, Maxam A (1973) The nucleotide sequence of the lac operator. Proc Natl Acad Sci USA
70:3581–3584
Gnirke A, Melnikov A, Maguire J et al (2009) Solution hybrid selection with ultra-long
oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189